Neurons in the cerebral cortex communicate with each other using highly specified, hierarchical rules of connectivity. There are more than 30 cell types in the neocortex, and these cell types can be differentiated by their developmental lineage, projection target, or expression of marker genes. Previous studies have attempted to reveal the logic of neural circuits by low-throughput anatomical or electrophysiological methods. Here we propose to develop and employ a novel trans-synaptic fluorescent complex formation strategy to chemically tag synapses defined by pre- and post- synaptic cell identity. Cell contacts made between genetically specified pre- and post- synaptic neurons will bring together a fluorescence-activating protein and one of a pair of covalently anchored fluorogenic dyes to trigger a 20,000-fold increase in fluorescence, easily detectable over background signal. The outstanding signal-to-noise and spectral properties of the dye will enable quantitative and in vivo analysis of cell-type specific synapses in the mammalian neocortex. We will use sequential labeling in different colors to differentially label newly formed synapses, allowing single endpoin measurement of synaptic density changes in response to experience. Applying these tools in the context of seizure models will reveal the cellular and molecular mechanism underlying changes in inhibition in cortex that result in increased seizure risk. The long- term goal of this proposal is to develop chemical biology tools for a complete index of cell-type specific synaptic contacts in order to establish how these contacts change in health and disease states.